Dear all, I was trying to map 76nt reads using Bowtie. I wanted to use the "seed" feature to avoid trimming off the adapter sequence.

1) this is the sequence that I trimmed off the last "4nt" long "adapter", which is not really the adapter, and I got it mapped.
HWUSI-EAS1621.1.2.1.5.745.0 16 chr1 173833971 255 72M * 0 0 CATCAGATAGGAGCGAAAGACTTAATATTGCTCATCAGCGTTAGTCTGCTGAACTATGTTATCATCATTGTA ;:;143>>=9:>:[email protected]@@=B<[email protected]@;?0>BA8>[email protected]@ABB<BBBABBAA?:?BACCBABB XA:i:0 MD:Z:72 NM:i:0